Polypoid primer software tools | Quantitative PCR data analysis

The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species.

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A pipeline that facilitates the design of primers in polyploid organisms. A web interface is available to design primers for hexaploid wheat. The use of PolyMarker reduces the time spent designing genome specific assays and highlighting homoeologous SNPs.

A web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer, and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users.

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